Category Archives: Uncategorized

The story behind the rats of NIMH

In 1982, there was a “not-from-Disney” animation that had fascinated me… “The Secret of NIMH.” Just discovering it root is bringing back memories. (Official Trailer.) In the 1971 book Ms. Frisby and the Rats of NIMH, written by Robert C. O’Brien, the rodents strive to create their own utopia after escaping from a research facility.… Read More »

Chateaubriand Fellowship for PhD students

Chateaubriand Fellowship The Chateaubriand Fellowship allows PhD students registered in an American university the opportunity to spend 4–9 months in France. The fellowship aims to initiate or reinforce collaborations or join projects between French and American research teams. US citizenship is not required (see eligibility and guidelines.) Summary French Government funded Chateaubriand STEM Fellowship available… Read More »

DataChat: Guided English Language© Ai and ML data analysis

A new spin-off company from the University of Wisconsin-Madison proposes a new interface for data analysis based on Guided English Language© (GEL) to command Artificial Intelligence and Machine Learning methods via “utterances” i.e. English-like phrases easier to write than code whether R, python, SQL, or other traditional tools. The web site is at datachat.ai The… Read More »

A Boy And His Atom: The World’s Smallest Movie

Moving atoms For some reason a paper copy of “Chemical and Engineering News” (November 11, 2019 – Vol 97 Issue 44) ended up in my hands, and I almost missed this fun section named: “30 years of moving atoms: How scanning probe microscopes revolutionized nanoscience” (link.) The article is progressing over time from 1993 til… Read More »

STAR index for human genome – overcoming the hardware barriers

Recently I was testing a Docker image to run a container for Next Gen sequencing, a way to test an existing “pipeline” on the first published study of the effect of the Zika virus. (https://hub.docker.com/r/maayanlab/zika/) Running a docker container may provide some ease in reproducibility, but sometimes there are also hardware barrier that need to… Read More »

Down-sampling FASTQ.gz paired ends

Downsampling I have performed a search for creating a set of down-sampled data from an actual  large dataset, and while there are many creative information on BioStar and other forums, I find that the most versatile and easy to use tool would be one recommended on the forums: seqtk which is available on Github: github.com/lh3/seqtk  Quoting… Read More »

asciinema: record commands in terminal

RE: asciinema.org  (Linux/MacOS) It may be nice to share/show commands being typed on a Text Terminal and embed this simple “movie” within blog or HTML page. It seems that the recording gets uploaded to their web site… Since it’s all text-based the file should be rather small and the clarity of replay very good compared… Read More »